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Amino Acid Sequence↗
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An approach to the collection and manipulation of time-based data using the IBM PC and BASICA.
With the advent of increasingly integrated, powerful and inexpensive digital electronics, relatively powerful computers have become available to the general public. Along with this technological boom there has been a concomitant increase in the availability of over-the-counter software packages which can be used by research scientists for program development. In the past, the development of computer programs for the collection of large amounts of time-based data was expensive and time consuming; however, the introduction of the current generation of 16-bit microcomputers and associated hardware and software packages has enabled investigators with only a rudimentary knowledge of computers and interfacing to begin to design programs. The schemes and algorithms, developed using BASICA on an IBM-Personal Computer, which are described in this article can serve other investigators as models for the assembly of their own programs for the collection, manipulation and plotting of time-based data. The incorporation of inexpensive computer graphics hardware and software, which provided a simple solution to the problem of analysis and presentation of large amounts of data, will also be discussed.
Algorithms↗
A computer system for analysis and integrated description of regulation of the molecular-genetic system of interferon induction and action.
A new theoretical approach to elaboration of an information-analytical integrated knowledge base containing data on regulation and function of biological systems is presented. The knowledge base incorporates: (i) a reference database containing experimental data on the structural-functional organization of a biological system; (ii) a dynamic mathematical model for analysis of the evolution of the system over time; and (iii) an interpretation module of simulation results. Application of this approach to theoretical investigation of the interferon system in the case of viral infection is discussed. The approach is specific in that it uses mathematical modeling technology, which allows one to generate mathematical models of different degrees of complexity in the analysis of the diverse aspects of biological system behavior. This approach allows one not only to store and to treat available experimental data, but also to acquire new knowledge about the behavior of a biological system. The proposed approach is implemented as a computer system for the IBM PC and compatibles.
Algorithms↗
Object-oriented programming for the biosciences.
The development of software systems for the biosciences is always closely connected to experimental practice. Programs must be able to handle the inherent complexity and heterogeneous structure of biological systems in combination with the measuring equipment. Moreover, a high degree of flexibility is required to treat rapidly changing experimental conditions. Object-oriented methodology seems to be well suited for this purpose. It enables an evolutionary approach to software development that still maintains a high degree of modularity. This paper presents experience with object-oriented technology gathered during several years of programming in the fields of bioprocess development and metabolic engineering. It concentrates on the aspects of experimental support, data analysis, interaction and visualization. Several examples are presented and discussed in the general context of the experimental cycle of knowledge acquisition, thus pointing out the benefits and problems of object-oriented technology in the specific application field of the biosciences. Finally, some strategies for future development are described.
Algorithms↗
RNAdraw: an integrated program for RNA secondary structure calculation and analysis under 32-bit Microsoft Windows.
The use of algorithms for calculation and analysis of RNA secondary structures has largely been limited to mainframe computers, mainly due to the 16-bit memory restrictions imposed by MS-DOS. The program presented here, RNAdraw, moves calculations to the 32-bit Microsoft Windows environments with an intuitive user interface with extensive viewing, editing and printing possibilities. The algorithms for secondary structure/basepair probability matrix/heat curve calculation have been ported directly from a 32-bit Unix environment. RNAdraw also offers novel features such as the options to edit energy parameters, extract structures of different probability levels, create de novo secondary structures interactively, and combine viewing of structures and basepair probabilities.
Algorithms↗
ONIX: an interactive PC program for the examination of protein 3D structure from PDB.
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Algorithms↗
Software for DNA sequencing by hybridization.
Sequencing by hybridization (SBH) is a promising alternative approach to DNA sequencing and mutation detection. Analysis of the resolving power of SBH involves rather difficult combinatorial and probabilistic problems, and sometimes computer simulation is the only way to estimate the parameters and limitations of SBH experiments. This paper describes a software package, DNA-SPECTRUM, which allows one to analyze the resolving power and parameters of SBH. We also introduce the technique for visualizing multiple SBH reconstructions and describe applications of DNA-SPECTRUM to estimate various SBH parameters. DNA-SPECTRUM is available at http://www-hto.usc.edu/software/sbh/index. html.
Base Sequence↗
Predicting RNA H-type pseudoknots with the massively parallel genetic algorithm.
MOTIVATION: Using the genetic algorithm (GA) for RNA folding on a massively parallel supercomputer, MasPar MP-2 with 16,384 processors, we successfully predicted the existence of H-type pseudoknots in several sequences. RESULTS: The GA is applied to folding the tRNA-like 3' end of turnip yellow mosaic virus (TYMV) RNA sequence with 82 nucleotides, the 3' UTRs of satellite tobacco necrosis virus (STNV)-2 RNA sequence with 619 nucleotides and STNV-I RNA sequence with 622 nucleotides, and the bacteriophage T2, T4 and T6 gene 32 mRNA sequences with 946, 1340 and 946 nucleotides, respectively. The GA's results match the phylogenetically supported tertiary structures of these sequences.
Algorithms↗
E-CELL: software environment for whole-cell simulation.
MOTIVATION: Genome sequencing projects and further systematic functional analyses of complete gene sets are producing an unprecedented mass of molecular information for a wide range of model organisms. This provides us with a detailed account of the cell with which we may begin to build models for simulating intracellular molecular processes to predict the dynamic behavior of living cells. Previous work in biochemical and genetic simulation has isolated well-characterized pathways for detailed analysis, but methods for building integrative models of the cell that incorporate gene regulation, metabolism and signaling have not been established. We, therefore, were motivated to develop a software environment for building such integrative models based on gene sets, and running simulations to conduct experiments in silico. RESULTS: E-CELL, a modeling and simulation environment for biochemical and genetic processes, has been developed. The E-CELL system allows a user to define functions of proteins, protein-protein interactions, protein-DNA interactions, regulation of gene expression and other features of cellular metabolism, as a set of reaction rules. E-CELL simulates cell behavior by numerically integrating the differential equations described implicitly in these reaction rules. The user can observe, through a computer display, dynamic changes in concentrations of proteins, protein complexes and other chemical compounds in the cell. Using this software, we constructed a model of a hypothetical cell with only 127 genes sufficient for transcription, translation, energy production and phospholipid synthesis. Most of the genes are taken from Mycoplasma genitalium, the organism having the smallest known chromosome, whose complete 580 kb genome sequence was determined at TIGR in 1995. We discuss future applications of the E-CELL system with special respect to genome engineering. AVAILABILITY: The E-CELL software is available upon request. SUPPLEMENTARY INFORMATION: The complete list of rules of the developed cell model with kinetic parameters can be obtained via our web site at: http://e-cell.org/.
Adenosine Triphosphate↗
bioWidgets: data interaction components for genomics.
MOTIVATION: The presentation of genomics data in a perspicuous visual format is critical for its rapid interpretation and validation. Relatively few public database developers have the resources to implement sophisticated front-end user interfaces themselves. Accordingly, these developers would benefit from a reusable toolkit of user interface and data visualization components. RESULTS: We have designed the bioWidget toolkit as a set of JavaBean components. It includes a wide array of user interface components and defines an architecture for assembling applications. The toolkit is founded on established software engineering design patterns and principles, including componentry, Model-View-Controller, factored models and schema neutrality. As a proof of concept, we have used the bioWidget toolkit to create three extendible applications: AnnotView, BlastView and AlignView.
Amino Acid Sequence↗
Arbor 3D: an interactive environment for examining phylogenetic and taxonomic trees in multiple dimensions.
UNLABELLED: This paper examines a new technique for the visualization of and the interaction with trees, objects frequently used to convey hierarchical relationships in biological data. Motivated by the quality of 2D tree interaction, we adapt the planar tree-of-life metaphor to a virtual, semi-immersive 3D environment. A 3D environment extends the utility of this metaphor by allowing the user to view an entire data set in a single screen. Interrogation of the tree is implemented using 3D input devices. This real-time interrogation of the tree itself provides a quick means by which to qualitatively analyse the hierarchical data. In this paper, we describe the techniques underlying the implementation of such an environment. We conclude by considering the utility of tree metaphors as a basis for the representation of highly dimensional data sets. AVAILABILITY: Arbor3D (source code, a binary executable for SGI IRIX 6.4, Perl parsers, and sample Newick data files) are available via the Internet (http://xian.tamu.edu/Arbor3D/). Arbor3D can be displayed in "CAVE simulator" mode on an SGI workstation screen, or as an interactive virtual environment on a projection workbench. CONTACT: druths@rice.edu; echen@cs.rice.edu; leland@xian.tamu.edu
Classification↗
The TRANSPATH signal transduction database: a knowledge base on signal transduction networks.
UNLABELLED: TRANSPATH is an information system on gene-regulatory pathways, and an extension module to the TRANSFAC database system (Wingender et al., Nucleic Acids Res., 28, 316-319, 2000). It focuses on pathways involved in the regulation of transcription factors in different species, mainly human, mouse and rat. Elements of the relevant signal transduction pathways like complexes, signaling molecules, and their states are stored together with information about their interaction in an object-oriented database. The database interface provides clickable maps and automatically generated pathway cascades as additional ways to explore the data. All information is validated with references to the original publications. Also, references to other databases are provided (TRANSFAC, SWISS-PROT, EMBL, PubMed and others). AVAILABILITY: The database is available over (http://transpath.gbf.de) for interactive perusal. As an exchange format for the data, eXtensible Markup Language (XML) flatfiles and a Document Type Definition (DTD) are provided.
Algorithms↗
Doing sequence analysis with your printer.
The software package RSVP (Rapid Sequence Visualization in PostScript) has a suite of visually oriented sequence analysis routines implemented entirely in the page description language PostScript, a widely used standard that is built into many printers. RSVP is thus a relatively platform-independent tool for providing a 'quick look' at sequence data, using form and color to help point out patterns, in advance of more sophisticated sequence analyses.
Amino Acid Sequence↗
GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems.
GEPASI is a software system for modelling chemical and biochemical reaction networks on computers running Microsoft Windows. For any system of up to 45 metabolites and 45 reactions, each with any user-defined or one of 35 predefined rate equations, one can produce trajectories of the metabolite concentrations and obtain a steady state (if it does exist). When steady-state solutions are produced, elasticity and control coefficients, as defined in metabolic control analysis, are calculated. GEPASI also allows the automatic generation of a sequence of simulations with different combinations of parameter values, effectively scanning a hyper-solid in parameter space. Together with the ability to produce user-defined columnar data files, these features allow for both very quick and systematic study of biochemical pathway models. The source code (in C) is available on request from the author, and while the user interface is dependent on having MS-Windows as the operating system, the numerical part is portable to other operating systems. GEPASI is suitable both for research and educational purposes. Although GEPASI was written with biochemical pathways in mind, it can equally be used to stimulate other dynamical systems.
Algorithms↗
Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations.
Cellerator describes single and multi-cellular signal transduction networks (STN) with a compact, optionally palette-driven, arrow-based notation to represent biochemical reactions and transcriptional activation. Multi-compartment systems are represented as graphs with STNs embedded in each node. Interactions include mass-action, enzymatic, allosteric and connectionist models. Reactions are translated into differential equations and can be solved numerically to generate predictive time courses or output as systems of equations that can be read by other programs. Cellerator simulations are fully extensible and portable to any operating system that supports Mathematica, and can be indefinitely nested within larger data structures to produce highly scaleable models.
Computer Graphics↗
FPV: fast protein visualization using Java 3D.
MOTIVATION: Many tools have been developed to visualize protein structures. Tools that have been based on Java 3D((TM)) are compatible among different systems and they can be run remotely through web browsers. However, using Java 3D for visualization has some performance issues with it. The primary concerns about molecular visualization tools based on Java 3D are in their being slow in terms of interaction speed and in their inability to load large molecules. This behavior is especially apparent when the number of atoms to be displayed is huge, or when several proteins are to be displayed simultaneously for comparison. RESULTS: In this paper we present techniques for organizing a Java 3D scene graph to tackle these problems. We have developed a protein visualization system based on Java 3D and these techniques. We demonstrate the effectiveness of the proposed method by comparing the visualization component of our system with two other Java 3D based molecular visualization tools. In particular, for van der Waals display mode, with the efficient organization of the scene graph, we could achieve up to eight times improvement in rendering speed and could load molecules three times as large as the previous systems could. AVAILABILITY: EPV is freely available with source code at the following URL: http://www.cs.ucsb.edu/~tcan/fpv/
Computer Graphics↗
New methods for joint analysis of biological networks and expression data.
SUMMARY: Biological networks, such as protein interaction, regulatory or metabolic networks, derived from public databases, biological experiments or text mining can be useful for the analysis of high-throughput experimental data. We present two algorithms embedded in the ToPNet application that show promising performance in analyzing expression data in the context of such networks. First, the Significant Area Search algorithm detects subnetworks consisting of significantly regulated genes. These subnetworks often provide hints on which biological processes are affected in the measured conditions. Second, Pathway Queries allow detection of networks including molecules that are not necessarily significantly regulated, such as transcription factors or signaling proteins. Moreover, using these queries, the user can formulate biological hypotheses and check their validity with respect to experimental data. All resulting networks and pathways can be explored further using the interactive analysis tools provided by ToPNet program.
Algorithms↗
A general computational model of mitochondrial metabolism in a whole organelle scale.
UNLABELLED: A computational tool for mitochondrial systems biology has been developed as a simulation model of E-Cell2, a publicly available simulation system. The general model consists of 58 enzymatic reactions and 117 metabolites, representing the respiratory chain, the TCA cycle, the fatty acid beta-oxidation and the inner-membrane transport system. It is based on previously published enzyme kinetics studies in the literature; we have successfully integrated and packaged them into a single large model. The model can be easily extended and modified so that mitochondrial biologists/physiologists can integrate their own models and evaluate them in the context of the whole organelle metabolism. AVAILABILITY: The mitochondrial model is bundled up with E-Cell2 simulation system, which can be downloaded from http://www.e-cell.org. CD-ROMs are also available and are distributed at major conferences. SUPPLEMENTARY INFORMATION: All the kinetic data are available via http://www.e-cell.org
Animals↗